Home

Welcome!

I am Annaël Brunet, this website is about my scientific research. I am very interested by research project focuses on the correlation between the dynamics of 3D chromosome folding organization and the role play by DNA-protein interaction inducing topological modifications or local interaction along polymer chain or changes in gene expression.

Research focus

If DNA is well-known for containing the genetic code essential to the cell physiology, its mechanical characteristics are now also under close study as they may actively participate to the different biological processes. Studying the spatial architecture and dynamics of the genomic material by taking into account the implication of modifications due to local effect (as transcriptional activity or inactivity of genes, intrinsic local curvature, induced DNA-protein bending) on the long range organization of the DNA material and on the DNA elastic response constitutes an important field of research to fully how chromosomes fold, move and interact.


Present project: The cell nucleus is well-known to be the localisation of main biological processes alight on the chromatin. Nowaday, the correlation between the spatial architecture of the genomic material and the dynamic of gene expression and regulation constitutes an important field of research. I'm investigating how mechanicals constraints induced by the 3D organisation of the biopolymer, as topological asociated domains (TADs) or lamins associated domains (LADs), cooperativly impact the chromatin elastic response and could guidance the variation in gene expresssion.

image
Conceptual schema of two compartementalized and compacted chromosome derived by interaction with nuclear lamina, in the nucleus

My work aims at both biostatistically analyzed RNA-Seq and Chip-Seq data to extract oscillating patterns in term of, respectively, gene expression or mechanicals constraints and modeling physical mechanisms which could mimic the 3D spacial variation of the chromatin biologically observed.

This work takes place in the laboratory:
- Collas Lab (head Leader : Collas Philippe) at the University of Oslo, Department of Molecular Medicine, Institute of Basic Medical Sciences Lab is in Oslo, Norway.


Thesis project: The DNA molecule commonly known as the double helix, is a biopolymer with a high degree of conformational and structural variability that participates in many biological processes. Some of them can be associated with local bending or local opening, local denaturation "bubble", of the double helix. Changes in temperature or salt concentration of the solution may also globally modify the physical properties of DNA molecules. During this work, we propose a joint theory-experiment high-throughput approach, corresponding to manage in parallel experimental technics, numerical simulations and, physics models, in order to get access to the value of a local bend angle, or to the magnitude of variations in the DNA rigidity parameter of this biomolecule on DNA samples with local defects or submitted to various physicochemical conditions.

image
From Broad Communications of Haley Bridger, August 5th, 2010

This work takes place in 2 laboratories:
- The Theoretical Physics Laboratory (LPT-IRSAMC) under the supervision of Nicolas Destainville in the Statistical Physics of Complex Systems group (head leader: Nicolas Destainville).
- The Institute of Pharmacology and Structural Biology under the supervision of Catherine Tardin in the Membrane and DNA dynamics team (head leader: Laurence Salomé).
Both labs are in Toulouse, South of France.

Check out my research page for more information.